fleas Targeted loci environmental. insect metagenome

The aim the study was to demonstrate differences in flea species microbiome and evaluate potential bias produced during genomic DNA isolation. We performed Ion Torrent PGM™ amplicon sequencing for the bacterial 16S rRNA gene to compare the microbiome of the ubiquitous cat flea (Ctenocephalides felis felis) and the Australian echidna stickfast flea (Echidnophaga ambulans ambulans). Protocols combining surface sterilisation with entire flea homogenisation or retaining flea exoskeleton to isolate genomic DNA were compared.